Gene set enrichment analysis (English Wikipedia)

Analysis of information sources in references of the Wikipedia article "Gene set enrichment analysis" in English language version.

refsWebsite

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arxiv.org

Tamayo P, Steinhardt G, Liberzon A, Mesirov JP (February 2016). "The limitations of simple gene set enrichment analysis assuming gene independence". Statistical Methods in Medical Research. 25 (1): 472–487. arXiv:1110.4128. doi:10.1177/0962280212460441. PMC 3758419. PMID 23070592.

bioconductor.org

"Org.Db Packages" – via Bioconductor.
Bolen C, Yaari G, Thakar J, Meng H, Turner J, Blankenship D, et al. (2017). "qusage: Quantitative Set Analysis for Gene Expression". doi:10.18129/B9.bioc.qusage – via Bioconductor.

biostars.org

"Gene Set Clustering based on Functional annotation (GeneSCF)". www.biostars.org.

broadinstitute.org

software.broadinstitute.org

"GSEA | Desktop Tutorial". software.broadinstitute.org.

doi.org

Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, et al. (October 2005). "Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles". Proceedings of the National Academy of Sciences of the United States of America. 102 (43): 15545–15550. doi:10.1073/pnas.0506580102. PMC 1239896. PMID 16199517.
Mootha VK, Lindgren CM, Eriksson KF, Subramanian A, Sihag S, Lehar J, et al. (July 2003). "PGC-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes". Nature Genetics. 34 (3): 267–273. doi:10.1038/ng1180. PMID 12808457. S2CID 13940856.
Maleki F, Ovens K, Hogan DJ, Kusalik AJ (2020). "Gene Set Analysis: Challenges, Opportunities, and Future Research". Frontiers in Genetics. 11: 654. doi:10.3389/fgene.2020.00654. PMC 7339292. PMID 32695141.
Liberzon A, Birger C, Thorvaldsdóttir H, Ghandi M, Mesirov JP, Tamayo P (December 2015). "The Molecular Signatures Database (MSigDB) hallmark gene set collection". Cell Systems. 1 (6): 417–425. doi:10.1016/j.cels.2015.12.004. PMC 4707969. PMID 26771021.
Tamayo P, Steinhardt G, Liberzon A, Mesirov JP (February 2016). "The limitations of simple gene set enrichment analysis assuming gene independence". Statistical Methods in Medical Research. 25 (1): 472–487. arXiv:1110.4128. doi:10.1177/0962280212460441. PMC 3758419. PMID 23070592.
Frost HR, Li Z, Moore JH (March 2015). "Spectral gene set enrichment (SGSE)". BMC Bioinformatics. 16 (1): 70. doi:10.1186/s12859-015-0490-7. PMC 4365810. PMID 25879888.
Vedi M, Nalabolu HS, Lin CW, Hoffman MJ, Smith JR, Brodie K, et al. (April 2022). "MOET: a web-based gene set enrichment tool at the Rat Genome Database for multiontology and multispecies analyses". Genetics. 220 (4). doi:10.1093/genetics/iyac005. PMC 8982048. PMID 35380657.
Yousif A, Drou N, Rowe J, Khalfan M, Gunsalus KC (June 2020). "NASQAR: a web-based platform for high-throughput sequencing data analysis and visualization". BMC Bioinformatics. 21 (1): 267. bioRxiv 10.1101/709980. doi:10.1186/s12859-020-03577-4. PMC 7322916. PMID 32600310.
Yu G, Wang LG, Han Y, He QY (May 2012). "clusterProfiler: an R package for comparing biological themes among gene clusters". Omics. 16 (5): 284–287. doi:10.1089/omi.2011.0118. PMC 3339379. PMID 22455463.
Tian F, Yang DC, Meng YQ, Jin J, Gao G (January 2020). "PlantRegMap: charting functional regulatory maps in plants". Nucleic Acids Research. 48 (D1): D1104–D1113. doi:10.1093/nar/gkz1020. PMC 7145545. PMID 31701126.
Liberzon A (2014). "A description of the Molecular Signatures Database (MSigDB) Web site". Stem Cell Transcriptional Networks. Methods in Molecular Biology. Vol. 1150. Clifton, N.J.: Springer. pp. 153–160. doi:10.1007/978-1-4939-0512-6_9. ISBN 978-1-4939-0511-9. PMID 24743996.
Chen EY, Tan CM, Kou Y, Duan Q, Wang Z, Meirelles GV, et al. (April 2013). "Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool". BMC Bioinformatics. 14: 128. doi:10.1186/1471-2105-14-128. PMC 3637064. PMID 23586463.
Kuleshov MV, Jones MR, Rouillard AD, Fernandez NF, Duan Q, Wang Z, et al. (July 2016). "Enrichr: a comprehensive gene set enrichment analysis web server 2016 update". Nucleic Acids Research. 44 (W1): W90–W97. doi:10.1093/nar/gkw377. PMC 4987924. PMID 27141961.
Xie Z, Bailey A, Kuleshov MV, Clarke DJ, Evangelista JE, Jenkins SL, et al. (March 2021). "Gene Set Knowledge Discovery with Enrichr". Current Protocols. 1 (3): e90. doi:10.1002/cpz1.90. PMC 8152575. PMID 33780170.
Subhash S, Kanduri C (September 2016). "GeneSCF: a real-time based functional enrichment tool with support for multiple organisms". BMC Bioinformatics. 17 (1): 365. doi:10.1186/s12859-016-1250-z. PMC 5020511. PMID 27618934.
Wadi L, Meyer M, Weiser J, Stein LD, Reimand J (August 2016). "Impact of outdated gene annotations on pathway enrichment analysis". Nature Methods. 13 (9): 705–706. doi:10.1038/nmeth.3963. PMC 7802636. PMID 27575621. S2CID 19548133.
Huang DA, Sherman BT, Lempicki RA (2009). "Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources". Nature Protocols. 4 (1): 44–57. doi:10.1038/nprot.2008.211. PMID 19131956. S2CID 10418677.
Huang DA, Sherman BT, Lempicki RA (1 December 2008). "Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources". Nature Protocols. 4 (1): 44–57. doi:10.1038/nprot.2008.211. PMID 19131956. S2CID 10418677.
Zhou Y, Zhou B, Pache L, Chang M, Khodabakhshi AH, Tanaseichuk O, et al. (April 2019). "Metascape provides a biologist-oriented resource for the analysis of systems-level datasets". Nature Communications. 10 (1): 1523. Bibcode:2019NatCo..10.1523Z. doi:10.1038/s41467-019-09234-6. PMC 6447622. PMID 30944313.
Blake JA, Christie KR, Dolan ME, Drabkin HJ, Hill DP, Ni L, et al. (Gene Ontology Consortium) (January 2015). "Gene Ontology Consortium: going forward". Nucleic Acids Research. 43 (Database issue): D1049–D1056. doi:10.1093/nar/gku1179. PMC 4383973. PMID 25428369.
McLean CY, Bristor D, Hiller M, Clarke SL, Schaar BT, Lowe CB, et al. (May 2010). "GREAT improves functional interpretation of cis-regulatory regions". Nature Biotechnology. 28 (5): 495–501. doi:10.1038/nbt.1630. PMC 4840234. PMID 20436461.
Pathan M, Keerthikumar S, Ang CS, Gangoda L, Quek CY, Williamson NA, et al. (August 2015). "FunRich: An open access standalone functional enrichment and interaction network analysis tool". Proteomics. 15 (15): 2597–2601. doi:10.1002/pmic.201400515. PMID 25921073. S2CID 28583044.
Berriz GF, King OD, Bryant B, Sander C, Roth FP (December 2003). "Characterizing gene sets with FuncAssociate". Bioinformatics (Oxford, England). 19 (18): 2502–4. doi:10.1093/bioinformatics/btg363. PMID 14668247.
Berriz GF, Beaver JE, Cenik C, Tasan M, Roth FP (November 2009). "Next generation software for functional trend analysis". Bioinformatics. 25 (22): 3043–3044. doi:10.1093/bioinformatics/btp498. PMC 2800365. PMID 19717575.
Chen J, Bardes EE, Aronow BJ, Jegga AG (July 2009). "ToppGene Suite for gene list enrichment analysis and candidate gene prioritization". Nucleic Acids Research. 37 (Web Server issue): W305–W311. doi:10.1093/nar/gkp427. PMC 2703978. PMID 19465376.
Yaari G, Bolen CR, Thakar J, Kleinstein SH (October 2013). "Quantitative set analysis for gene expression: a method to quantify gene set differential expression including gene-gene correlations". Nucleic Acids Research. 41 (18): e170. doi:10.1093/nar/gkt660. PMC 3794608. PMID 23921631.
Turner JA, Bolen CR, Blankenship DM (August 2015). "Quantitative gene set analysis generalized for repeated measures, confounder adjustment, and continuous covariates". BMC Bioinformatics. 16: 272. doi:10.1186/s12859-015-0707-9. PMC 4551517. PMID 26316107.
Avey S, Cheung F, Fermin D, Frelinger J, Gaujoux R, Gottardo R, et al. (HIPC-CHI Signatures Project Team, HIPC-I Consortium) (August 2017). "Multicohort analysis reveals baseline transcriptional predictors of influenza vaccination responses". Science Immunology. 2 (14): eaal4656. doi:10.1126/sciimmunol.aal4656. PMC 5800877. PMID 28842433.
Bolen C, Yaari G, Thakar J, Meng H, Turner J, Blankenship D, et al. (2017). "qusage: Quantitative Set Analysis for Gene Expression". doi:10.18129/B9.bioc.qusage – via Bioconductor.
Conesa A, Götz S, García-Gómez JM, Terol J, Talón M, Robles M (September 2005). "Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research". Bioinformatics. 21 (18): 3674–3676. doi:10.1093/bioinformatics/bti610. PMID 16081474.
Berriz GF, King OD, Bryant B, Sander C, Roth FP (December 2003). "Characterizing gene sets with FuncAssociate". Bioinformatics. 19 (18). Oxford, England: 2502–4. doi:10.1093/bioinformatics/btg363. PMID 14668247.
Holden M, Deng S, Wojnowski L, Kulle B (December 2008). "GSEA-SNP: applying gene set enrichment analysis to SNP data from genome-wide association studies". Bioinformatics. 24 (23): 2784–2785. doi:10.1093/bioinformatics/btn516. PMID 18854360.
Manuck TA, Watkins S, Esplin MS, Parry S, Zhang H, Huang H, et al. (2016). "242: Gene set enrichment investigation of maternal exome variation in spontaneous preterm birth (SPTB)". American Journal of Obstetrics and Gynecology. 214 (1): S142–S143. doi:10.1016/j.ajog.2015.10.280.
Maruschke M, Hakenberg OW, Koczan D, Zimmermann W, Stief CG, Buchner A (January 2014). "Expression profiling of metastatic renal cell carcinoma using gene set enrichment analysis". International Journal of Urology. 21 (1): 46–51. doi:10.1111/iju.12183. PMID 23634695. S2CID 33377555.
Hass J, Walton E, Wright C, Beyer A, Scholz M, Turner J, et al. (June 2015). "Associations between DNA methylation and schizophrenia-related intermediate phenotypes - a gene set enrichment analysis". Progress in Neuro-Psychopharmacology & Biological Psychiatry. 59: 31–39. doi:10.1016/j.pnpbp.2015.01.006. PMC 4346504. PMID 25598502.
Elovainio M, Taipale T, Seppälä I, Mononen N, Raitoharju E, Jokela M, et al. (December 2015). "Activated immune-inflammatory pathways are associated with long-standing depressive symptoms: Evidence from gene-set enrichment analyses in the Young Finns Study". Journal of Psychiatric Research. 71: 120–125. doi:10.1016/j.jpsychires.2015.09.017. PMID 26473696.

funrich.org

"FunRich :: Download". funrich.org.

geneontology.org

amigo.geneontology.org

Gene Ontology Consortium. "AmiGO 2: Welcome". amigo.geneontology.org.

harvard.edu

ui.adsabs.harvard.edu

Zhou Y, Zhou B, Pache L, Chang M, Khodabakhshi AH, Tanaseichuk O, et al. (April 2019). "Metascape provides a biologist-oriented resource for the analysis of systems-level datasets". Nature Communications. 10 (1): 1523. Bibcode:2019NatCo..10.1523Z. doi:10.1038/s41467-019-09234-6. PMC 6447622. PMID 30944313.

intermine.readthedocs.io

"List enrichment widgets statistics — InterMine documentation".

kandurilab.org

genescf.kandurilab.org

"GeneSCF::Gene Set Clustering based on Functional annotation". genescf.kandurilab.org.

metascape.org

"Metascape". metascape.org. Retrieved 20 December 2019.

mssm.edu

labs.icahn.mssm.edu

"Ma'ayan Laboratory - Computational Systems Biology - Icahn School of Medicine at Mount Sinai". labs.icahn.mssm.edu. 19 September 2023.

nature.com

"Figure 3: Heatmaps of gene set enrichment analysis (GSEA) of DEGs based on RNAseq data in response to abiotic stresses". www.nature.com. Retrieved 2018-09-05.

ncifcrf.gov

david.ncifcrf.gov

DAVID release and version information, DAVID Bioinformatics Resources 6.8

nih.gov

pubmed.ncbi.nlm.nih.gov

Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, et al. (October 2005). "Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles". Proceedings of the National Academy of Sciences of the United States of America. 102 (43): 15545–15550. doi:10.1073/pnas.0506580102. PMC 1239896. PMID 16199517.
Mootha VK, Lindgren CM, Eriksson KF, Subramanian A, Sihag S, Lehar J, et al. (July 2003). "PGC-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes". Nature Genetics. 34 (3): 267–273. doi:10.1038/ng1180. PMID 12808457. S2CID 13940856.
Maleki F, Ovens K, Hogan DJ, Kusalik AJ (2020). "Gene Set Analysis: Challenges, Opportunities, and Future Research". Frontiers in Genetics. 11: 654. doi:10.3389/fgene.2020.00654. PMC 7339292. PMID 32695141.
Liberzon A, Birger C, Thorvaldsdóttir H, Ghandi M, Mesirov JP, Tamayo P (December 2015). "The Molecular Signatures Database (MSigDB) hallmark gene set collection". Cell Systems. 1 (6): 417–425. doi:10.1016/j.cels.2015.12.004. PMC 4707969. PMID 26771021.
Tamayo P, Steinhardt G, Liberzon A, Mesirov JP (February 2016). "The limitations of simple gene set enrichment analysis assuming gene independence". Statistical Methods in Medical Research. 25 (1): 472–487. arXiv:1110.4128. doi:10.1177/0962280212460441. PMC 3758419. PMID 23070592.
Frost HR, Li Z, Moore JH (March 2015). "Spectral gene set enrichment (SGSE)". BMC Bioinformatics. 16 (1): 70. doi:10.1186/s12859-015-0490-7. PMC 4365810. PMID 25879888.
Vedi M, Nalabolu HS, Lin CW, Hoffman MJ, Smith JR, Brodie K, et al. (April 2022). "MOET: a web-based gene set enrichment tool at the Rat Genome Database for multiontology and multispecies analyses". Genetics. 220 (4). doi:10.1093/genetics/iyac005. PMC 8982048. PMID 35380657.
Yousif A, Drou N, Rowe J, Khalfan M, Gunsalus KC (June 2020). "NASQAR: a web-based platform for high-throughput sequencing data analysis and visualization". BMC Bioinformatics. 21 (1): 267. bioRxiv 10.1101/709980. doi:10.1186/s12859-020-03577-4. PMC 7322916. PMID 32600310.
Yu G, Wang LG, Han Y, He QY (May 2012). "clusterProfiler: an R package for comparing biological themes among gene clusters". Omics. 16 (5): 284–287. doi:10.1089/omi.2011.0118. PMC 3339379. PMID 22455463.
Tian F, Yang DC, Meng YQ, Jin J, Gao G (January 2020). "PlantRegMap: charting functional regulatory maps in plants". Nucleic Acids Research. 48 (D1): D1104–D1113. doi:10.1093/nar/gkz1020. PMC 7145545. PMID 31701126.
Liberzon A (2014). "A description of the Molecular Signatures Database (MSigDB) Web site". Stem Cell Transcriptional Networks. Methods in Molecular Biology. Vol. 1150. Clifton, N.J.: Springer. pp. 153–160. doi:10.1007/978-1-4939-0512-6_9. ISBN 978-1-4939-0511-9. PMID 24743996.
Chen EY, Tan CM, Kou Y, Duan Q, Wang Z, Meirelles GV, et al. (April 2013). "Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool". BMC Bioinformatics. 14: 128. doi:10.1186/1471-2105-14-128. PMC 3637064. PMID 23586463.
Kuleshov MV, Jones MR, Rouillard AD, Fernandez NF, Duan Q, Wang Z, et al. (July 2016). "Enrichr: a comprehensive gene set enrichment analysis web server 2016 update". Nucleic Acids Research. 44 (W1): W90–W97. doi:10.1093/nar/gkw377. PMC 4987924. PMID 27141961.
Xie Z, Bailey A, Kuleshov MV, Clarke DJ, Evangelista JE, Jenkins SL, et al. (March 2021). "Gene Set Knowledge Discovery with Enrichr". Current Protocols. 1 (3): e90. doi:10.1002/cpz1.90. PMC 8152575. PMID 33780170.
Subhash S, Kanduri C (September 2016). "GeneSCF: a real-time based functional enrichment tool with support for multiple organisms". BMC Bioinformatics. 17 (1): 365. doi:10.1186/s12859-016-1250-z. PMC 5020511. PMID 27618934.
Wadi L, Meyer M, Weiser J, Stein LD, Reimand J (August 2016). "Impact of outdated gene annotations on pathway enrichment analysis". Nature Methods. 13 (9): 705–706. doi:10.1038/nmeth.3963. PMC 7802636. PMID 27575621. S2CID 19548133.
Huang DA, Sherman BT, Lempicki RA (2009). "Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources". Nature Protocols. 4 (1): 44–57. doi:10.1038/nprot.2008.211. PMID 19131956. S2CID 10418677.
Huang DA, Sherman BT, Lempicki RA (1 December 2008). "Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources". Nature Protocols. 4 (1): 44–57. doi:10.1038/nprot.2008.211. PMID 19131956. S2CID 10418677.
Zhou Y, Zhou B, Pache L, Chang M, Khodabakhshi AH, Tanaseichuk O, et al. (April 2019). "Metascape provides a biologist-oriented resource for the analysis of systems-level datasets". Nature Communications. 10 (1): 1523. Bibcode:2019NatCo..10.1523Z. doi:10.1038/s41467-019-09234-6. PMC 6447622. PMID 30944313.
Blake JA, Christie KR, Dolan ME, Drabkin HJ, Hill DP, Ni L, et al. (Gene Ontology Consortium) (January 2015). "Gene Ontology Consortium: going forward". Nucleic Acids Research. 43 (Database issue): D1049–D1056. doi:10.1093/nar/gku1179. PMC 4383973. PMID 25428369.
McLean CY, Bristor D, Hiller M, Clarke SL, Schaar BT, Lowe CB, et al. (May 2010). "GREAT improves functional interpretation of cis-regulatory regions". Nature Biotechnology. 28 (5): 495–501. doi:10.1038/nbt.1630. PMC 4840234. PMID 20436461.
Pathan M, Keerthikumar S, Ang CS, Gangoda L, Quek CY, Williamson NA, et al. (August 2015). "FunRich: An open access standalone functional enrichment and interaction network analysis tool". Proteomics. 15 (15): 2597–2601. doi:10.1002/pmic.201400515. PMID 25921073. S2CID 28583044.
Berriz GF, King OD, Bryant B, Sander C, Roth FP (December 2003). "Characterizing gene sets with FuncAssociate". Bioinformatics (Oxford, England). 19 (18): 2502–4. doi:10.1093/bioinformatics/btg363. PMID 14668247.
Berriz GF, Beaver JE, Cenik C, Tasan M, Roth FP (November 2009). "Next generation software for functional trend analysis". Bioinformatics. 25 (22): 3043–3044. doi:10.1093/bioinformatics/btp498. PMC 2800365. PMID 19717575.
Chen J, Bardes EE, Aronow BJ, Jegga AG (July 2009). "ToppGene Suite for gene list enrichment analysis and candidate gene prioritization". Nucleic Acids Research. 37 (Web Server issue): W305–W311. doi:10.1093/nar/gkp427. PMC 2703978. PMID 19465376.
Yaari G, Bolen CR, Thakar J, Kleinstein SH (October 2013). "Quantitative set analysis for gene expression: a method to quantify gene set differential expression including gene-gene correlations". Nucleic Acids Research. 41 (18): e170. doi:10.1093/nar/gkt660. PMC 3794608. PMID 23921631.
Turner JA, Bolen CR, Blankenship DM (August 2015). "Quantitative gene set analysis generalized for repeated measures, confounder adjustment, and continuous covariates". BMC Bioinformatics. 16: 272. doi:10.1186/s12859-015-0707-9. PMC 4551517. PMID 26316107.
Avey S, Cheung F, Fermin D, Frelinger J, Gaujoux R, Gottardo R, et al. (HIPC-CHI Signatures Project Team, HIPC-I Consortium) (August 2017). "Multicohort analysis reveals baseline transcriptional predictors of influenza vaccination responses". Science Immunology. 2 (14): eaal4656. doi:10.1126/sciimmunol.aal4656. PMC 5800877. PMID 28842433.
Conesa A, Götz S, García-Gómez JM, Terol J, Talón M, Robles M (September 2005). "Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research". Bioinformatics. 21 (18): 3674–3676. doi:10.1093/bioinformatics/bti610. PMID 16081474.
Berriz GF, King OD, Bryant B, Sander C, Roth FP (December 2003). "Characterizing gene sets with FuncAssociate". Bioinformatics. 19 (18). Oxford, England: 2502–4. doi:10.1093/bioinformatics/btg363. PMID 14668247.
Holden M, Deng S, Wojnowski L, Kulle B (December 2008). "GSEA-SNP: applying gene set enrichment analysis to SNP data from genome-wide association studies". Bioinformatics. 24 (23): 2784–2785. doi:10.1093/bioinformatics/btn516. PMID 18854360.
Maruschke M, Hakenberg OW, Koczan D, Zimmermann W, Stief CG, Buchner A (January 2014). "Expression profiling of metastatic renal cell carcinoma using gene set enrichment analysis". International Journal of Urology. 21 (1): 46–51. doi:10.1111/iju.12183. PMID 23634695. S2CID 33377555.
Hass J, Walton E, Wright C, Beyer A, Scholz M, Turner J, et al. (June 2015). "Associations between DNA methylation and schizophrenia-related intermediate phenotypes - a gene set enrichment analysis". Progress in Neuro-Psychopharmacology & Biological Psychiatry. 59: 31–39. doi:10.1016/j.pnpbp.2015.01.006. PMC 4346504. PMID 25598502.
Elovainio M, Taipale T, Seppälä I, Mononen N, Raitoharju E, Jokela M, et al. (December 2015). "Activated immune-inflammatory pathways are associated with long-standing depressive symptoms: Evidence from gene-set enrichment analyses in the Young Finns Study". Journal of Psychiatric Research. 71: 120–125. doi:10.1016/j.jpsychires.2015.09.017. PMID 26473696.

ncbi.nlm.nih.gov

Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, et al. (October 2005). "Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles". Proceedings of the National Academy of Sciences of the United States of America. 102 (43): 15545–15550. doi:10.1073/pnas.0506580102. PMC 1239896. PMID 16199517.
Maleki F, Ovens K, Hogan DJ, Kusalik AJ (2020). "Gene Set Analysis: Challenges, Opportunities, and Future Research". Frontiers in Genetics. 11: 654. doi:10.3389/fgene.2020.00654. PMC 7339292. PMID 32695141.
Liberzon A, Birger C, Thorvaldsdóttir H, Ghandi M, Mesirov JP, Tamayo P (December 2015). "The Molecular Signatures Database (MSigDB) hallmark gene set collection". Cell Systems. 1 (6): 417–425. doi:10.1016/j.cels.2015.12.004. PMC 4707969. PMID 26771021.
Tamayo P, Steinhardt G, Liberzon A, Mesirov JP (February 2016). "The limitations of simple gene set enrichment analysis assuming gene independence". Statistical Methods in Medical Research. 25 (1): 472–487. arXiv:1110.4128. doi:10.1177/0962280212460441. PMC 3758419. PMID 23070592.
Frost HR, Li Z, Moore JH (March 2015). "Spectral gene set enrichment (SGSE)". BMC Bioinformatics. 16 (1): 70. doi:10.1186/s12859-015-0490-7. PMC 4365810. PMID 25879888.
Vedi M, Nalabolu HS, Lin CW, Hoffman MJ, Smith JR, Brodie K, et al. (April 2022). "MOET: a web-based gene set enrichment tool at the Rat Genome Database for multiontology and multispecies analyses". Genetics. 220 (4). doi:10.1093/genetics/iyac005. PMC 8982048. PMID 35380657.
Yousif A, Drou N, Rowe J, Khalfan M, Gunsalus KC (June 2020). "NASQAR: a web-based platform for high-throughput sequencing data analysis and visualization". BMC Bioinformatics. 21 (1): 267. bioRxiv 10.1101/709980. doi:10.1186/s12859-020-03577-4. PMC 7322916. PMID 32600310.
Yu G, Wang LG, Han Y, He QY (May 2012). "clusterProfiler: an R package for comparing biological themes among gene clusters". Omics. 16 (5): 284–287. doi:10.1089/omi.2011.0118. PMC 3339379. PMID 22455463.
Tian F, Yang DC, Meng YQ, Jin J, Gao G (January 2020). "PlantRegMap: charting functional regulatory maps in plants". Nucleic Acids Research. 48 (D1): D1104–D1113. doi:10.1093/nar/gkz1020. PMC 7145545. PMID 31701126.
Chen EY, Tan CM, Kou Y, Duan Q, Wang Z, Meirelles GV, et al. (April 2013). "Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool". BMC Bioinformatics. 14: 128. doi:10.1186/1471-2105-14-128. PMC 3637064. PMID 23586463.
Kuleshov MV, Jones MR, Rouillard AD, Fernandez NF, Duan Q, Wang Z, et al. (July 2016). "Enrichr: a comprehensive gene set enrichment analysis web server 2016 update". Nucleic Acids Research. 44 (W1): W90–W97. doi:10.1093/nar/gkw377. PMC 4987924. PMID 27141961.
Xie Z, Bailey A, Kuleshov MV, Clarke DJ, Evangelista JE, Jenkins SL, et al. (March 2021). "Gene Set Knowledge Discovery with Enrichr". Current Protocols. 1 (3): e90. doi:10.1002/cpz1.90. PMC 8152575. PMID 33780170.
Subhash S, Kanduri C (September 2016). "GeneSCF: a real-time based functional enrichment tool with support for multiple organisms". BMC Bioinformatics. 17 (1): 365. doi:10.1186/s12859-016-1250-z. PMC 5020511. PMID 27618934.
Wadi L, Meyer M, Weiser J, Stein LD, Reimand J (August 2016). "Impact of outdated gene annotations on pathway enrichment analysis". Nature Methods. 13 (9): 705–706. doi:10.1038/nmeth.3963. PMC 7802636. PMID 27575621. S2CID 19548133.
Zhou Y, Zhou B, Pache L, Chang M, Khodabakhshi AH, Tanaseichuk O, et al. (April 2019). "Metascape provides a biologist-oriented resource for the analysis of systems-level datasets". Nature Communications. 10 (1): 1523. Bibcode:2019NatCo..10.1523Z. doi:10.1038/s41467-019-09234-6. PMC 6447622. PMID 30944313.
Blake JA, Christie KR, Dolan ME, Drabkin HJ, Hill DP, Ni L, et al. (Gene Ontology Consortium) (January 2015). "Gene Ontology Consortium: going forward". Nucleic Acids Research. 43 (Database issue): D1049–D1056. doi:10.1093/nar/gku1179. PMC 4383973. PMID 25428369.
McLean CY, Bristor D, Hiller M, Clarke SL, Schaar BT, Lowe CB, et al. (May 2010). "GREAT improves functional interpretation of cis-regulatory regions". Nature Biotechnology. 28 (5): 495–501. doi:10.1038/nbt.1630. PMC 4840234. PMID 20436461.
Berriz GF, Beaver JE, Cenik C, Tasan M, Roth FP (November 2009). "Next generation software for functional trend analysis". Bioinformatics. 25 (22): 3043–3044. doi:10.1093/bioinformatics/btp498. PMC 2800365. PMID 19717575.
Chen J, Bardes EE, Aronow BJ, Jegga AG (July 2009). "ToppGene Suite for gene list enrichment analysis and candidate gene prioritization". Nucleic Acids Research. 37 (Web Server issue): W305–W311. doi:10.1093/nar/gkp427. PMC 2703978. PMID 19465376.
Yaari G, Bolen CR, Thakar J, Kleinstein SH (October 2013). "Quantitative set analysis for gene expression: a method to quantify gene set differential expression including gene-gene correlations". Nucleic Acids Research. 41 (18): e170. doi:10.1093/nar/gkt660. PMC 3794608. PMID 23921631.
Turner JA, Bolen CR, Blankenship DM (August 2015). "Quantitative gene set analysis generalized for repeated measures, confounder adjustment, and continuous covariates". BMC Bioinformatics. 16: 272. doi:10.1186/s12859-015-0707-9. PMC 4551517. PMID 26316107.
Avey S, Cheung F, Fermin D, Frelinger J, Gaujoux R, Gottardo R, et al. (HIPC-CHI Signatures Project Team, HIPC-I Consortium) (August 2017). "Multicohort analysis reveals baseline transcriptional predictors of influenza vaccination responses". Science Immunology. 2 (14): eaal4656. doi:10.1126/sciimmunol.aal4656. PMC 5800877. PMID 28842433.
Hass J, Walton E, Wright C, Beyer A, Scholz M, Turner J, et al. (June 2015). "Associations between DNA methylation and schizophrenia-related intermediate phenotypes - a gene set enrichment analysis". Progress in Neuro-Psychopharmacology & Biological Psychiatry. 59: 31–39. doi:10.1016/j.pnpbp.2015.01.006. PMC 4346504. PMID 25598502.

nyu.edu

nasqar.abudhabi.nyu.edu

"NASQAR: Nucleic Acid SeQuence Analysis Resource".

researchgate.net

"Molecular signature database (MSigDB) 3.0 (PDF Download Available)". ResearchGate.

semanticscholar.org

api.semanticscholar.org

Mootha VK, Lindgren CM, Eriksson KF, Subramanian A, Sihag S, Lehar J, et al. (July 2003). "PGC-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes". Nature Genetics. 34 (3): 267–273. doi:10.1038/ng1180. PMID 12808457. S2CID 13940856.
Wadi L, Meyer M, Weiser J, Stein LD, Reimand J (August 2016). "Impact of outdated gene annotations on pathway enrichment analysis". Nature Methods. 13 (9): 705–706. doi:10.1038/nmeth.3963. PMC 7802636. PMID 27575621. S2CID 19548133.
Huang DA, Sherman BT, Lempicki RA (2009). "Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources". Nature Protocols. 4 (1): 44–57. doi:10.1038/nprot.2008.211. PMID 19131956. S2CID 10418677.
Huang DA, Sherman BT, Lempicki RA (1 December 2008). "Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources". Nature Protocols. 4 (1): 44–57. doi:10.1038/nprot.2008.211. PMID 19131956. S2CID 10418677.
Pathan M, Keerthikumar S, Ang CS, Gangoda L, Quek CY, Williamson NA, et al. (August 2015). "FunRich: An open access standalone functional enrichment and interaction network analysis tool". Proteomics. 15 (15): 2597–2601. doi:10.1002/pmic.201400515. PMID 25921073. S2CID 28583044.
Maruschke M, Hakenberg OW, Koczan D, Zimmermann W, Stief CG, Buchner A (January 2014). "Expression profiling of metastatic renal cell carcinoma using gene set enrichment analysis". International Journal of Urology. 21 (1): 46–51. doi:10.1111/iju.12183. PMID 23634695. S2CID 33377555.

stanford.edu

bejerano.stanford.edu

"GREAT Input: Genomic Regions Enrichment of Annotations Tool". Bejerano Lab. Stanford University. Archived from the original on 3 December 2018.

web.archive.org

"GREAT Input: Genomic Regions Enrichment of Annotations Tool". Bejerano Lab. Stanford University. Archived from the original on 3 December 2018.

webgestalt.org

"WebGestalt (WEB-based GEne SeT AnaLysis Toolkit)". www.webgestalt.org.